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Li VR, Zhang Z, Troyanskaya OG. CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes. Bioinformatics. 2021 ;37(Suppl_1):i342-i348.
Metsky HC, Welch NL, Pillai PP, Haradhvala NJ, Rumker L, Mantena S, et al. Designing sensitive viral diagnostics with machine learning. Nat Biotechnol. 2022 ;40(7):1123-1131.
Yao V, Wong AK, Troyanskaya OG. Enabling Precision Medicine through Integrative Network Models. J Mol Biol. 2018 ;430(18 Pt A):2913-2923.
Pereira TD, Aldarondo DE, Willmore L, Kislin M, Wang SS-H, Murthy M, et al. Fast animal pose estimation using deep neural networks. Nat Methods. 2019 ;16(1):117-125.
Machens CK, Romo R, Brody CD. Flexible control of mutual inhibition: a neural model of two-interval discrimination. Science. 2005 ;307(5712):1121-4.
Jun JK, Miller P, Hernández A, Zainos A, Lemus L, Brody CD, et al.. Heterogenous population coding of a short-term memory and decision task. J Neurosci. 2010 ;30(3):916-29.
Sohrabi S, Mor DE, Kaletsky R, Keyes W, Murphy CT. High-throughput behavioral screen in C. elegans reveals Parkinson's disease drug candidates. Commun Biol. 2021 ;4(1):203.
Seyboldt R, Lavoie J, Henry A, Vanaret J, Petkova MD, Gregor T, et al. Latent space of a small genetic network: Geometry of dynamics and information. Proc Natl Acad Sci U S A. 2022 ;119(26):e2113651119.
Piet AT, Erlich JC, Kopec CD, Brody CD. Rat Prefrontal Cortex Inactivations during Decision Making Are Explained by Bistable Attractor Dynamics. Neural Comput. 2017 ;29(11):2861-2886.
Markowitz DA, Collman F, Brody CD, Hopfield JJ, Tank DW. Rate-specific synchrony: using noisy oscillations to detect equally active neurons. Proc Natl Acad Sci U S A. 2008 ;105(24):8422-7.
Chen KM, Cofer EM, Zhou J, Troyanskaya OG. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019 ;16(4):315-318.